A 47-year-old man, who was the operator of a nightclub on West 43d Street, was shot to death early yesterday morning as he stood outside his car on Third Avenue, the police said. The man, Theodore Fay, a resident of 30 Waterside Plaza in Manhattan, was shot once or twice in the back at 3:55 A.M., the police said, as he stood outside his 1986 Lincoln near the corner of Third Avenue and East 37th Street. Two Bronx residents were arrested soon after the shooting and charged with second-degree murder, said Capt. Edward Minogue. Although a motive had yet to be established, Captain Minogue said robbery apparently was not the cause of the shooting. Mr. Fay was carrying $1,200 when he was killed, the captain said. An officer close to the investigation, who spoke on the condition his name not be used, said the police are examining two possible motives. ''We are looking at what kind of business he was in and the business associates he had,'' the officer said. ''And we are looking at a possible narcotics connection on the part of one of the shooters.'' Although the police would not describe the club, the Midtown Club at 127 West 43d Street, a bartender interviewed there yesterday afternoon said its clientele is primarily gay black men.

Two more suspects were arrested yesterday and charged with murder in the slaying last month of a midtown Manhattan nighclub operator, the police said. One of the suspects was indentified as Spiros Varsos, 52 years old, of 301 West 53d Street in Clinton, the owner of a vending-machine company. He was arrested outside his home at 12:30 P.M., according to Capt. Edward Minogue, chief of detectives in the midtown area. Captain Minogue said the arrest was ''based on information from witnesses.'' * * * Captain Minogue said Mr. Varsos paid the two gunman $8,000 to kill Mr. Fay ''for unknown reasons.'' ''There is no clear-cut motive,'' he said. He said neither the victim nor any of the suspects had links to organized crime. * * * Captain Minogue said Mr. Varsos owned the Big Apple Vending Machine Company in Astoria, Queens, and ''apparently did business with Fay.'' He said Mr. Fay managed a number of clubs in Manhattan in which Mr. Varsos had his vending machines.

According to Robert Russo who testified at the murder trial in 1988, Spiros Varsos allegedly "had organized crime connections" as reported by William Glaberson in an April 26, 1990 article ("Prisoner Tells Of Confession By Defendant") for The New York Times.